Workflow

With narration in mind, copy/paste bits and pieces of text/equations and graphics as PDF into Keynote, and set up sequential "builds." Save as foovid.key.

Record narration (as voice1.aif) with Sound Studio. Put a few extra seconds of silence at the front.

In Keynote, "record" slideshow in foovid.key while playing voice1.aif. (Mic picks up low quality sound from speakers.) Export recorded slideshow as QuickTime movie (with no compression) named foovid.mov.

Open foovid.mov in QuickTime Pro. Extract the audio track from foovid.mov and export it as trashme.aif. Open that in Sound Studio and note the time at which the first sound begins (within 0.1 sec or so). Then trash it.

Open voice1.aif in Sound Studio, and delete silence at the beginning so that the first sound begins at the noted time. Save.

Open foovid.movandvoice1.aif in QuickTime Pro.

Add voice1.aif to foovid.mov as a second audio track. Listen to see if the alignment is close enough. If so, delete the first one.

Edit foovid.mov to fix any problems with the flow of the video track. Each edit will affect the audio track, but that's okay---replace the editted audio track with voice1.aif.
It may also be convenient or necessary to edit voice1.aif in Sound Studio at this stage. (The better step 4 went, the less there will be to do here. If there's a lot to fix, you may be better off redoing steps 4-6.)

Notes and Caveats

There are numerous alternatives to Sound Studio, including Audacity. I like Sound Studio because of its dynamics compression and noise gate expansion. Audacity's noise removal works very well, while Sound Studio doesn't do noise removal.

Sound Studio has a really nasty bug that causes it not to respond to menu requests (like Save!) after you've worked for a long time without saving changes. Beware.

There's no particular reason for using .aif as the working sound format.

Tips for editting in QuickTime Pro:

The Movie Inspector pane (command-I) displays the current time in hundredths of seconds.

Select None (command-B) is extremely useful for putting the selection boundaries at the current time.

To delay a transition for x seconds, select x seconds prior to it; copy, and paste. Then delete x seconds after the transition.

To make a transition occur x seconds sooner, select x seconds prior to it and delete. Then select x seconds after the transition; copy, and paste.

The Movie Properties pane (command-J) is where you work with separate tracks. (Extract, delete, etc.)

To add an audio track, first Select All and Copy from the audio; then at the beginning of the movie choose "Add to Movie" from the Edit menu.